On 12 September 2013 19:54, Schmidt, Stephan <[email protected]> wrote: > Dear all, > > I managed to compile all packages as specified in the dorsal lion.package > file and dorsal reports all is well. Unfortunately, the import of dolfin in > python fails: >
Mismatched Python versions is perhaps the biggest installation problem on OSX. > Python 2.7.5 (default, Aug 24 2013, 04:50:09) > [GCC 4.2.1 Compatible Apple Clang 3.0 (tags/Apple/clang-211.12)] on darwin > Type "help", "copyright", "credits" or "license" for more information. >>>> from dolfin import * > Fatal Python error: Interpreter not initialized (version mismatch?) > Abort trap: 6 > > I am using > which python > /opt/local/bin/python > > which I think is supposed to be the correct (Mac Ports) Version of python. > Any help is greatly appreciated. > Did you clean out all the FEniCS components before running Dorsal again? The development version should pick up the Python library that matches the Python interpreter. Garth > Regards, > Stephan > > On 12 Sep 2013, at 16:03, Garth N. Wells wrote: > >> On 12 September 2013 15:22, Schmidt, Stephan <[email protected]> >> wrote: >>> Thank you for your support! Just a quick clarification: Are you referring >>> to the development version of FEniCS that can be enabled in dorsal.cfg >> >> Yes, but I don't use Dorsal. I install manually (cloning each of the >> FEniCS projects). >> >> (I have been using that and it gives the same error messages) or is >> there also a development version of dorsal? >>> >> >> You can also get a development version of Dorsal at >> https://bitbucket.org/fenics-project/dorsal. >> >> Garth >> >>> A MacPorts port would be much appreciated! >>> >>> Regards, >>> Stephan Schmidt >>> >>> Am 12.09.2013 um 14:20 schrieb "Garth N. Wells" <[email protected]>: >>> >>>> I'd recommend using the development version - it has quite a few build >>>> fixes for OSX. >>>> >>>> I build DOLFIN under OSX 10.8, but I don't use Dorsal. You can get >>>> almost everything you need from Macports. To make it work, I: >>>> >>>> 1. Install all the available dependencies via Macports >>>> 2. Set default gcc/g++ to GCC 4.7 or 4.8 (there is a Macports command >>>> that is easy to find on the net, but I don't recall it) >>>> 3. Set default Python toy python2.7 via Macports >>>> 4. Set compiler variables: >>>> >>>> export OMPI_CC=gcc >>>> export OMPI_CXX=g++ >>>> export CXX=g++ >>>> export CC=gcc >>>> >>>> From memory, the only Macports package that may give you trouble is >>>> Armadillo, which you may need to installed by hand. >>>> >>>> There is a Macports 'port' in the works. >>>> >>>> Garth >>>> >>>> On 12 September 2013 12:05, Schmidt, Stephan <[email protected]> >>>> wrote: >>>>> Dear all, >>>>> >>>>> I was re-directed here after posting an installation specific question >>>>> here: >>>>> http://fenicsproject.org/qa/1186/how-to-build-and-install-fenics-using-dorsal-on-osx-10-7 >>>>> >>>>> In the meantime, I figured out that these error messages: >>>>> >>>>> Building CXX object dolfin/CMakeFiles/dolfin.dir/adaptivity/adapt.cpp.o >>>>> In file included from /opt/local/include/boost/mpi/config.hpp:20, >>>>> from /opt/local/include/boost/mpi/allocator.hpp:15, >>>>> from /opt/local/include/boost/mpi.hpp:22, >>>>> from >>>>> /Users/sschmidt/Documents/FEniCS/src/dolfin-1.2.0/dolfin/common/MPI.h:35, >>>>> from >>>>> /Users/sschmidt/Documents/FEniCS/src/dolfin-1.2.0/dolfin/fem/UFCCell.h:31, >>>>> from >>>>> /Users/sschmidt/Documents/FEniCS/src/dolfin-1.2.0/dolfin/fem/FiniteElement.h:27, >>>>> from >>>>> /Users/sschmidt/Documents/FEniCS/src/dolfin-1.2.0/dolfin/adaptivity/adapt.cpp:24: >>>>> /opt/local/include/openmpi/mpi.h:367: error: wrong number of arguments >>>>> specified for ‘deprecated’ attribute >>>>> >>>>> stem from the fact that dorsal is always using the gcc compiler in >>>>> >>>>> /usr/bin/gcc --version >>>>> i686-apple-darwin11-llvm-gcc-4.2 (GCC) 4.2.1 (Based on Apple Inc. build >>>>> 5658) (LLVM build 2336.1.00) >>>>> Copyright (C) 2007 Free Software Foundation, Inc. >>>>> This is free software; see the source for copying conditions. There is NO >>>>> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR >>>>> PURPOSE. >>>>> >>>>> which is llvm-gcc-4.2 and that cannot handle those ‘deprecated’ >>>>> attributes. In the meantime, I managed to compile dolfin by enforcing the >>>>> use of >>>>> >>>>> /opt/local/bin/gcc --version >>>>> gcc (MacPorts gcc48 4.8.1_3) 4.8.1 >>>>> Copyright (C) 2013 Free Software Foundation, Inc. >>>>> This is free software; see the source for copying conditions. There is NO >>>>> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR >>>>> PURPOSE. >>>>> >>>>> which does handle those ‘deprecated’ attribute and dolfin seems to work >>>>> fine! >>>>> >>>>> However, I noticed dorsal uses many tricks to always use /usr/bin/gcc. I >>>>> thought changing >>>>> #export CC=/usr/bin/gcc >>>>> #export CXX=/usr/bin/g++ >>>>> export CC=/opt/local/bin/gcc >>>>> export CXX=/opt/local/bin/g++ >>>>> >>>>> and >>>>> #Change mpicc (which is always mpicc built upon llvm-gcc-4.2 to mpicc >>>>> built upon gcc-4.8 >>>>> #for CMD in /opt/local/bin/openmpi* >>>>> #do >>>>> # ln -sf ${CMD} ${INSTALL_PATH}/bin/`basename ${CMD} | cut -b 5-` >>>>> #done >>>>> for CMD in /Users/sschmidt/Documents/FEniCS/MyOpenMPI/bin/openmpi* >>>>> do >>>>> ln -sf ${CMD} ${INSTALL_PATH}/bin/`basename ${CMD} | cut -b 5-` >>>>> done >>>>> >>>>> in /platforms/supported/lion.platform would change this behaviour, but >>>>> this seems not to work. I still have to add >>>>> -DCMAKE_CXX_COMPILER:STRING=g++ \ >>>>> -DCMAKE_C_COMPILER:STRING=gcc \ >>>>> -DCMAKE_Fortran_COMPILER:STRING=gfortran " >>>>> >>>>> to all .package-files in order to make dorsal use the default compiler >>>>> gcc-4.8, which can handle ‘deprecated’ attributes. >>>>> >>>>> Thus, I would much appreciate it, if you could give a hint on what is the >>>>> recommended compiler for dolfin and how to easily set the compiler for >>>>> all .package-files. >>>>> Many thanks for any helping with this! >>>>> >>>>> _______________________________________________ >>>>> fenics-support mailing list >>>>> [email protected] >>>>> http://fenicsproject.org/mailman/listinfo/fenics-support > _______________________________________________ fenics-support mailing list [email protected] http://fenicsproject.org/mailman/listinfo/fenics-support
